XtraCrysPy

A Python tool for visualizing atomic systems and spatial properties of condensed matter.

Features:

• Plot molecular systems with minimal setup
• Plot systems from DFT or MD input/output files
• Interact with the system to caluclate distances, angles, or receive atomic information
• Display relaxation or MD steps from QE relax output, raw coordinates, LAMMPS trajectory files, or CP2K (xyz)
• Animate trajectories, with control over frames per second and steps per frame.
• Display reciprocal space features
• Plot real space iso-surfaces (charge density, etc)
• Plot reciprocal iso-surfaces (Fermi surface, spin-texture, etc)

Supported File Types:

• Quantum ESPRESSO input or output
• POSCAR
• CIF
• XSF
• CP2K
• BXSF
• Any ASE supported format

Requirements:

• python 3.8
• numpy 1.19
• fury 0.8
• ase

Installation:

The Anaconda Python distribution is recommended.

Install with pip:

• pip install xtracryspy

Install from source:

• python setup.py install
• python setup.py install --user

(only use --user if you do not have permission to install python packages)

Display atomic models directly from the command line:

• xcp --help
• xcp -fn <input_file> -ff <file_format> -bl <bond_distance>

Control Inputs:

• 'u' : Toggle UI visibility
• 'a' : Toggle Axis visibility
• 'b' : Toggle Boundary visiblity
• 'c' : Toggle constraint of atoms within cell
• 'k' : Toggle the reciprocal lattice vector visibility
• 's' : Togle the selection type panel visibility
• 'n' : Toggle the cell repition panel visibility
• '>' : Step forward in relax or MD
• '<' : Step backward in relax or MD
• CTRL + ('>' or '<') : Step 5% through the relaxation or MD steps
• SPACE : Pause or resume an active animation
• SHIFT + 'o' : Report the camera position and orientation
• SHIFT + 'c' : Reset camera to default position
• SHIFT + 's' : Take snapshot
• CTRL + 'w' : Exit
• Arrow Keys : Rotate model
• SHIFT + Arrow Keys : Translate camera
• CTRL + Arrow Keys (+ SHIFT) : Rotate (or Translate) in smaller steps

Display an atomic model from inputfile, with the examples/main.py script:

• python main.py <input_file>
• python main.py <input_file> <bond_distance>

Examples:

Available in the examples directory

From scratch:

• python CNO3.py
• python caffeine.py
• python silicon_fcc.py
• python example_motion.py
• python example_textured_isosurface.py

From inputfile (with main.py script):

• python main.py <input_file>
• python main.py <input_file> <bond_distance>

From inputfile (programmatic):

• python SnTe_2D.py
• python example_cif.py
• python example_cp2k.py
• python example_qe_in.py
• python example_poscar.py

Relax QE outputfile:

• python example_relax.py

LAMMPS MD trajectory:

• python example_lammps_md.py

Charge Density:

• python example_charge_density.py

Reciprocal Space:

• python example_BZ.py

Isosurfaces:

• python example_isosurface1.py
• python example_isosurface2.py
• python example_isosurface_clip.py
• python example_colored_isosurface.py
• python example_textured_isosurface.py
• python example_textured_isosurface_clip.py